Re: [HTCondor-users] submitted jobs are not running

[Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>]

In terminal opened by condor_submit, the variable $FSLDIR and I  
suppose also other fsl-based variables are not known.

I have tried to copy my .bashrc file to /home/condor folder which I  
have created, but it did not help. Of course, I have changed owner of  
the folder and files inside at condor:mri (condor belongs to mri group).

Any other ideas why terminal opened by condor does not know variables  
defined by my .bashrc file? And how to fix it?

Rene



Cituji Labounek Renà <xlabou01@xxxxxxxxxxxxxxxxxx>:

> Ben,
>
> you are right in error file is written something like that:
>
> slice_0033.error:
> /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: 1:  
> /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: /bin/zeropad: not  
> found
> /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: 76:  
> /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh: /bin/xfibres: not  
> found
>
> I undertand it can not find two other libraries zeropad and xfibres,  
> but when I am running the slice_0033.sh script (Executable in  
> condor_submit) directly in terminal, the script works well.
>
> labounek@emperor:~/test/dti.bedpostX/condor_logs$ ./slice_0033.sh
> labounek@emperor:~/test/dti.bedpostX/condor_logs$
>
> slice_0033.sh:
> #!/bin/sh
> /usr/share/fsl/5.0/bin/bedpostx_single_slice.sh  
> /home/labounek/test/dti 33 --nf=3 --fudge=1 --bi=1000 --nj=1250  
> --se=25 --model=2 --cnonlinear
>
> So unfortunately, I am still lost :-( Could the problem be e.g. the  
> Universe? Or should I set something more in slice_0033.condor file?
>
> slice_0033.condor:
> Executable = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.sh
> Universe = vanilla
> Output = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.out
> Error = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.error
> Log   = /home/labounek/test/dti.bedpostX/condor_logs/slice_0033.log
> Queue
>
> Kind Regards,
> Rene
>
> Cituji Ben Cotton <ben.cotton@xxxxxxxxxxxxxxxxxx>:
>
> > Rene,
> >
> > The output suggests that your jobs ran and completed very quickly. If
> > you have Output and Error defined in your submit file, I'd look in
> > those locations to see what output your job produced. That may give
> > you an indication of why it completed so quickly.
> >
> >
> > Thanks,
> > BC
> >
> > --
> > Ben Cotton